Published January 20, 2018 | Version v1
Dataset Open

AFLP dataset and sequence alignments from a study of Rhododendron ferrugineum across the whole species range.

Authors/Creators

  • 1. W. Szafer Institute of Botany, Polish Academy of Sciences, ul. Lubicz 46, 31-512 Kraków, Poland
  • 2. Department of Botany, Institute of Environmental Biology, University of Wrocław, ul. Kanonia 6/8, 52-328 Wrocław, Poland

Description

STRUCTURE DATASET

The raw data are in the files:

  1. Rfe_KAR_AAT-CAC2_2017-10-18-16-55-16.zip
  2. Rfe_KAR_ATC-CAC_2017-10-25-12-39-28.zip
  3. Rfe_KAR_ATG-CTG2_2017-10-24-09-40-25.zip

Population data: populations.txt

The final structure file: Rfe.str

We analysed the obtained results in GeneMapper (Applied Biosystems) with default settings for AFLP analysis. The combinations of selective starters amplified the following numbers of polymorphic markers: AAT-CAC=127 (mean=40,4; SD=8,1), ATC-CAC=119 (mean=35,3; SD=5,4), ATG-CTG=144 (mean=44,4; SD=5,0). The blank samples yielded 0, 6 and 5 markers, respectively, which were removed from the final data matrix. We also removed the markers present in only one individual. Three samples (one from each of the populations L22, K27 and S05) failed to amplify in one of the selective primer reactions and were thus removed from the final matrix. The estimated error rate was 2.87% and the final matrix comprises of 87 individuals and 254 polymorphic loci.

SEQUENCE ALIGNMENTS

  1. Rfe_ITS_align.fas
  2. Rfe_rpl32-trnL_align.fas 
  3. Rfe_RPS12-RPL20_align.fas 
  4. Rfe_trnfM-trnS_align.fas      
  5. Rfe_trnLF_align.fas 

Files

populations.txt

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